In that case I will file that into my box of complaints where the game never explains anything. :(
I don't really get it either. I'm guessing on your screen at the top 2/3rd of the HP bar is the "shield" you see on other players. When you take heavy damage the last third turns red, I think this is the bottom HP bar you see on players. So two thirds for shields, one third of actual HP. Though I don't think it even matters since it all acts as HP. Why they show two HP bars on enemy players? I have no idea.
I could be wrong but I believe the reasoning is that you don't get bonus damage for headshots until you remove the shield part with the exception of snipers which do enough damage to break the shield and then still headshot after.
The easiest way to win in my experience is to use the Kestrel B layout and get a decent boarding party. I almost never bother with drones other than maybe a single defense drone. For the boss I've had the most success with teleporting two people each into the triple ion shot weapon and the triple missile weapon rooms. After you take those out teleport into the triple laser room and once you take that out the boss can't hurt you for the rest of phase 1. You can then shoot your way through the shields and take out the healing room so that you can teleport back into the main part of the ship and take out all of the crew except for the guy manning the beam weapon all the way on the right. If you take out all the crew now they can't board you later making the later phases easier as long as you leave that last guy alive so that the computer doesn't take control of the ship. For the other two phases you pretty much just repeat teleporting into the weapon rooms and taking them out as soon as possible and you should win pretty easily. The only thing you really have to worry about is the missiles getting a lucky hit on your weapons or shields before you take them out especially on phase 3 as you try to burn down the super shields. Also I would highly recommend always getting a cloaking device since it is incredibly helpful for dealing with the phase 2 drone waves or the phase 3 laser blasts.